VMD-L Mailing List

From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Fri Oct 31 2008 - 16:39:17 CDT

Do you mean "for viewing a model" or as in "for linking a fusion
protein"? If it's a model, why do you need explicit conformation? If
its the latter: look at the literature on single-chain
immunoglobulins: multiples of GGGGS mostly. Energy minimization will
not improve on that.
Cheers,

Boris

On 31-Oct-08, at 3:07 PM, Edward Lyman wrote:

> Dear all,
>
> I am trying to think of a way to find a conformation of a linker,
> consisting of 6 or so residues, that is consistent with the fixed
> orientation of two domains on either side. Ideally I could fix the
> two domains and then run some sort of MC or MD based optimization
> to get a reasonable starting configuration for the linker. A less
> satisfactory way would be to rotate a dihedral, and the rest of the
> domain along with it, and just look at it and see if i like it.
>
> Thnx,
> Ed Lyman
>